Water geometry

Oppo D. W. and Horowitz M. (2000) Glacial deep water geometry South Atlantic benthic foraminiferal Cd/Ca and S C evidence. Paleoceanography 15, 147-160. 

Table 12.7 lists the structural properties of the hydration shell of UOjfaq) and UO (aq). For the purposes of comparison, past experimental and theoretical data for the first shell of AnO (An = U, Np, Pu) are also reported in Table 12.7. The hydration shell structure of UO (aq) has been described in detail elsewhere [150] so we will focus on the shell structure of UOjfaq). As shown in Figure 12.8, the AIMD simulations indicate that the first shell of UOjfaq) has five water molecules in the equatorial plane, in contrast to the QM/MM prediction of 4.51. The predicted U(V)=0< distance is very close to previous measurements of other actinyl(V) ions (Np(V) and Pu( V)) and are greater than the previous predicted value by 0.07A. Also, our average first-shell U-0 bond distance is slightly longer than the previous simulated value, which is expected since the first shell of the AIMD simulations contains more water ligands. Previous gas-phase structures exhibit slightly longer bonds as expected. Relative to UO (aq), UO Caq) shows a lengthening of 0.08A and 0.1 A for the U=Oai and bonds, respectively, because of reduced electrostatic attraction. Other first-shell properties of UOjfaq) and UO faq), such as the intramolecular water geometry and tilt angles, compare closely.

Therefore, so-called decorated models are used. In a famous paper that appeared in 1997, Ninham and Yaminsky proposed the consideration of dispersion forces in addition to electrostatic interactions and short-range repulsive interactions coming from the finite volume of the ions. To do so, they based their model on the Poisson-Boltzmann (PB) equation. The dispersion forces were derived from a Lifehitz-like approach. The merit of Ninham and Yaminsky s idea is to bring in quite naturally ion specificity and to explain also differences of ion behaviour near different interfaces, such as at the air-water and the water-oil interfaces. However, in the meantime it turned out that this approach is oversimplified. Especially, the neglect of the water geometry around ions and close to surfaces is a serious problem that can even lead to qualitatively wrong thermodynamic results. 

This theory, when applied to the SPC water geometry but with a fixed dipole equal to that of an isolated H2O molecule, p = 1.85D, leads to the result = 2.62D. This is in good agreement with the well-known extended simple point charged model SPC/E which allows for the polarisation correction. This validates the self-consistent mean-field procedure. As an illustration of the anion polarisation effect. Fig. 7... 

The Champ-Sons model has been developed to quantitatively predict the field radiated by water- or solid wedge- eoupled transdueers into solids. It is required to deal with interfaces of complex geometry, arbitrary transducers and arbitrary excitation pulses. It aims at computing the time-dependent waveform of various acoustical quantities (displacement, velocity, traction, velocity potential) radiated at a (possibly large) number of field-points inside a solid medium. 

Apparently a negative AP with Q < 90° can be found for particular pore geometries [53]. A different type of water repellency is desired to prevent the deterioration of blacktop roads consisting of crushed rock coated with bituminous materials. Here the problem is that water tends to spread into the stone-oil interface, detaching the aggregate from its binder [54]. No entirely satisfactory solution has been found, although various detergent-type additives have been found to help. Much more study of the problem is needed. 

Figure Cl.3.7. Equilibrium geometries of some water clusters from ah initio calculations. (Taken from 1621.)...

An important area that has yet to be fully explored is the effect of the flexibility of water molecules. The intennolecular forces in water are large enough to cause significant distortions from the gas-phase monomer geometry. In addition, the flexibility is cmcial in any description of vibrational excitation in water. 

HyperChem uses th e ril 31 water m odel for solvation. You can place th e solute in a box of T1P3P water m oleeules an d impose periodic boun dary eon dition s. You may then turn off the boundary conditions for specific geometry optimi/.aiion or molecular dynamics calculations. However, th is produces undesirable edge effects at the solvent-vacuum interface. 

IlypcrChem cannot perform a geometry optinii/.aiioii or molecular dynamics simulation using Cxien ded Iliickel. Stable molecules can collapse, with nuclei piled on top of one another, or they can dissociate in to atoms. With the commonly used parameters, the water molecule is predicted to be linear. 

One can start building up a list of MM3 parameters by use of the TINKER analyze command. Don t expect to build up the entire set, which occupies about 100 pages in the MM3 user s manual, but do obtain a few representative examples to get an idea of how a parameter set is constr ucted. From previous exercises and projects, you should have input and output geometries for an alkene, an alkane, and water. From these, the object is to determine the stretching and bending parameters for the C—C, C=C, C—H, and O—H bonds. The C—H bond parameters are not the same... 

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